# Full workflow

## Modular

%%{init: {"flowchart": {"htmlLabels": false}} }%%
graph LR
    classDef opt stroke-dasharray: 5

    subgraph TemplateFlow
        template["Template"]:::opt
    end

    subgraph raw[Raw dataset]
      T1w
      bold[BOLD]
      sbref["Single-band
             reference"]:::opt
      fmap[Fieldmap]:::opt
    end

    subgraph anat[Anatomical fit]
    direction LR
      norm["T1w-to-template
            transform"]:::opt
    end

    subgraph min[BOLD fit]
    direction LR
      coreg["BOLD-to-T1w
             transform"]
      hmc["HMC
           transforms"]
      boldref_coreg["Coregistration
                     reference"]
      bold2fmap["BOLD-fieldmap
                 transform"]:::opt
      boldref_hmc["Motion
                   correction
                   reference"]
      fmap'["Preprocessed
             Fieldmap"]:::opt
    end

    subgraph Transform;
       direction LR;
       stc(["Slice-timing
             correction"]):::opt
       fmap''["Resampled
               Fieldmap"]:::opt
       boldr["Resampled
              BOLD"]
    end

    template -.-> norm
    T1w -.-> norm
    norm -.-> boldr
    T1w --> coreg
    bold --- stc;
    bold --> hmc
    bold --> boldref_hmc ---> hmc
    fmap -.-> fmap' -.-> boldref_coreg
    boldref_hmc & fmap' -..-> bold2fmap
    boldref_hmc --> boldref_coreg --> coreg
    sbref -.-> boldref_coreg
    boldref_coreg ~~~ bold2fmap -.-> boldref_coreg

    stc & hmc --> boldr
    bold2fmap & fmap' -.-> fmap''
    coreg & fmap'' -.-> boldr

## Monolithic

%%{init: {"flowchart": {"htmlLabels": false}} }%%
graph LR
    classDef opt stroke-dasharray: 5

    subgraph TemplateFlow
        template["Template"]:::opt
    end

    subgraph raw[Raw dataset]
      T1w
      bold[BOLD]
      sbref["Single-band
             reference"]:::opt
      fmap[Fieldmap]:::opt
    end

    subgraph fmriprep[Preprocessing]
    direction LR
      norm["T1w-to-template
            transform"]:::opt
      coreg["BOLD-to-T1w
             transform"]
      hmc["HMC
           transforms"]
      boldref_coreg["Coregistration
                     reference"]
      bold2fmap["BOLD-fieldmap
                 transform"]:::opt
      boldref_hmc["Motion
                   correction
                   reference"]
      fmap'["Preprocessed
             fieldmap"]:::opt
       stc(["Slice-timing
             correction"]):::opt
       fmap''["Resampled
               fieldmap"]:::opt
       boldr["Resampled
              BOLD"]
    end

    template & T1w -.-> norm -.-> boldr

    T1w --> coreg
    bold --> boldref_hmc ----> hmc
    bold --> hmc
    boldref_hmc --> boldref_coreg --> coreg
    fmap -.-> fmap'
    boldref_hmc & fmap' -.-> bold2fmap
    sbref -.-> boldref_coreg

    bold --- stc;
    stc & hmc --> boldr
    bold2fmap & fmap' -.-> fmap'' -.-> boldref_coreg
    coreg & fmap'' -.-> boldr

# Fit workflows

## Anat and func

%%{init: {"flowchart": {"htmlLabels": false}} }%%
graph LR
    classDef opt stroke-dasharray: 5

    subgraph TemplateFlow
        template["Template"]:::opt
    end

    subgraph raw[Raw dataset]
      T1w
      bold[BOLD]
      sbref["Single-band
             reference"]:::opt
      fmap[Fieldmap]:::opt
    end

    subgraph anat[Anatomical fit]
    direction LR
      norm["T1w-to-template
            transform"]:::opt
    end

    template -..-> norm
    T1w -...-> norm

    subgraph min[BOLD fit]
    direction LR
      coreg["BOLD-to-T1w
             transform"]
      hmc["HMC
           transforms"]
      boldref_coreg["Coregistration
                     reference"]
      bold2fmap["BOLD-fieldmap
                 transform"]:::opt
      boldref_hmc["Motion
                   correction
                   reference"]
      fmap'["Preprocessed
             Fieldmap"]:::opt
    end

    T1w ----> coreg
    bold --> boldref_hmc ---> hmc
    bold --> hmc
    boldref_hmc --> boldref_coreg --> coreg
    fmap -.-> fmap' -.-> boldref_coreg
    boldref_hmc & fmap' -..-> bold2fmap
    sbref -.-> boldref_coreg
    boldref_coreg ~~~ bold2fmap -.-> boldref_coreg

## Anat only

%%{init: {"flowchart": {"htmlLabels": false}} }%%
graph LR
    classDef opt stroke-dasharray: 5

    subgraph TemplateFlow
        template["Template"]
    end

    subgraph raw[Raw dataset]
      T1w
    end

    subgraph anat[Anatomical fit]
    direction LR
      norm["T1w-to-template
            transform"]
    end

    template & T1w --> norm

## Func only

%%{init: {"flowchart": {"htmlLabels": false}} }%%
graph LR
    classDef opt stroke-dasharray: 5

    subgraph raw[Raw dataset]
      T1w
      bold[BOLD]
      sbref["Single-band
             reference"]:::opt
      fmap[Fieldmap]:::opt
    end

    subgraph min[BOLD fit]
    direction LR
      coreg["BOLD-to-T1w
             transform"]
      hmc["HMC
           transforms"]
      boldref_coreg["Coregistration
                     reference"]
      bold2fmap["BOLD-fieldmap
                 transform"]:::opt
      boldref_hmc["Motion
                   correction
                   reference"]
      fmap'["Preprocessed
             Fieldmap"]:::opt
    end

    T1w ----> coreg
    bold --> boldref_hmc ---> hmc
    bold --> hmc
    boldref_hmc --> boldref_coreg --> coreg
    fmap -.-> fmap' -.-> boldref_coreg
    boldref_hmc & fmap' -..-> bold2fmap
    sbref -.-> boldref_coreg
    boldref_coreg ~~~ bold2fmap -.-> boldref_coreg

# Transform workflow

%%{init: {"flowchart": {"htmlLabels": false}} }%%
graph LR
    classDef opt stroke-dasharray: 5

    subgraph raw[Raw dataset]
      bold[BOLD]
    end
    
    subgraph min[Fit derivatives]
      norm["T1w-to-template
            transform"]
      coreg["BOLD-to-T1w
             transform"]
      hmc["HMC
           transforms"]
      bold2fmap["BOLD-fieldmap
                 transform"]:::opt
      fmap'["Preprocessed
             Fieldmap"]:::opt
    end

    %% subgraph "`**Archive**`"
    %%   raw & min
    %% end

    subgraph Transform;
       direction LR;
       stc(["Slice-timing
             correction"]):::opt
       fmap''["Resampled
               Fieldmap"]:::opt
       boldr["Resampled
              BOLD"]
    end
    bold --- stc;
    norm & coreg -.-> boldr
    stc & hmc --> boldr
    bold2fmap & fmap' -.-> fmap''
    fmap'' -.-> boldr

# Old

graph LR;
    classDef opt stroke-dasharray: 5

    subgraph raw[Raw dataset];
      direction TB;
      T1w & fmap[Fieldmap]:::opt & bold[BOLD]
      sbref["Single-band
             reference"]:::opt
    end
    
    subgraph min[Fit derivatives];
      direction TB;
      T1w ------> norm["T1w-to-template
                     transform"]
      boldref_coreg & T1w --> coreg
      bold --> boldref_hmc["Initial BOLD
                        Reference"]
      boldref_hmc --> boldref_coreg
      sbref & fmap'' -.-> boldref_coreg["Final BOLD
                                         Reference"]
      bold & boldref_hmc ----> hmc["HMC
                              transforms"]
      boldref_coreg --> boldmask["BOLD mask"]
      coreg["BOLD-to-T1w
             transform"]
      fmap' & boldref_hmc -...-> bold2fmap["BOLD-fieldmap
                                  transform"]
      fmap -.-> fmap'["Preprocessed
                      Fieldmap"]
      fmap' -.-> fmap''["Resampled
                         Fieldmap"]
    end

graph LR
    classDef opt stroke-dasharray: 5

    subgraph TemplateFlow
        template["Template"]
    end

    subgraph raw[Raw dataset]
      T1w
      bold[BOLD]
      sbref["Single-band
             reference"]:::opt
      fmap[Fieldmap]:::opt
    end
    
    subgraph min[Fit derivatives]
      norm["T1w-to-template
            transform"]
      coreg["BOLD-to-T1w
             transform"]
      hmc["HMC
           transforms"]
      boldref_coreg["Final BOLD
                     Reference"]
      bold2fmap["BOLD-fieldmap
                 transform"]:::opt
      boldref_hmc["Initial BOLD
                   Reference"]
      fmap'["Preprocessed
             Fieldmap"]:::opt

      T1w ----> norm & coreg
      bold --> boldref_hmc ---> hmc
      bold --> hmc
      boldref_hmc --> boldref_coreg --> coreg
      fmap -.-> fmap' -.-> boldref_coreg
      boldref_hmc & fmap' -..-> bold2fmap
      sbref -.-> boldref_coreg
    boldref_coreg ~~~ bold2fmap -.-> boldref_coreg
    end

    template ----> norm

### Fixup

graph LR
    classDef opt stroke-dasharray: 5

    subgraph "Manual fixes"
      t1w_brain["Brain Mask"]
      bold2fmap["BOLD-fieldmap
                 transform"]
    end

    subgraph TemplateFlow
        template["Template"]
    end

    subgraph raw[Raw dataset]
      T1w
      bold[BOLD]
      sbref["Single-band
             reference"]:::opt
      fmap[Fieldmap]:::opt
    end
    
    subgraph min[Fit derivatives]
      norm["T1w-to-template
            transform"]
      coreg["BOLD-to-T1w
             transform"]
      hmc["HMC
           transforms"]
      boldref_coreg["Final BOLD
                     Reference"]
      boldref_hmc["Initial BOLD
                   Reference"]
      fmap'["Preprocessed
             Fieldmap"]:::opt

      t1w_brain ----> norm
      T1w ----> norm & coreg
      bold --> boldref_hmc ---> hmc
      bold --> hmc
      boldref_hmc --> boldref_coreg --> coreg
      fmap -.-> fmap' -.-> boldref_coreg
      boldref_hmc & fmap'
      sbref -.-> boldref_coreg
      bold2fmap --> boldref_coreg
    end

    template ----> norm

### Optional template

%%{init: {"flowchart": {"htmlLabels": false}} }%%
graph LR
    classDef opt stroke-dasharray: 5

    subgraph TemplateFlow
        template["Template"]:::opt
    end

    subgraph raw[Raw dataset]
      T1w
      bold[BOLD]
      sbref["Single-band
             reference"]:::opt
      fmap[Fieldmap]:::opt
    end
    
    subgraph min[Fit derivatives]
      norm["T1w-to-template
            transform"]:::opt
      coreg["BOLD-to-T1w
             transform"]
      hmc["HMC
           transforms"]
      boldref_coreg["Final BOLD
                     Reference"]
      bold2fmap["BOLD-fieldmap
                 transform"]:::opt
      boldref_hmc["Initial BOLD
                   Reference"]
      fmap'["Preprocessed
             Fieldmap"]:::opt

      T1w -...-> norm
      T1w ----> coreg
      bold --> boldref_hmc ---> hmc
      bold --> hmc
      boldref_hmc --> boldref_coreg --> coreg
      fmap -.-> fmap' -.-> boldref_coreg
      boldref_hmc & fmap' -..-> bold2fmap
      sbref -.-> boldref_coreg
    boldref_coreg ~~~ bold2fmap -.-> boldref_coreg
    end

    template -...-> norm

### Bold preproc

%%{init: {"flowchart": {"htmlLabels": false}} }%%
graph LR
    classDef opt stroke-dasharray: 5

    subgraph raw[Raw dataset]
      T1w
      bold[BOLD]
      sbref["Single-band
             reference"]:::opt
      fmap[Fieldmap]:::opt
    end
    
    subgraph min[Fit derivatives]
      coreg["BOLD-to-T1w
             transform"]
      hmc["HMC
           transforms"]
      boldref_coreg["Final BOLD
                     Reference"]
      bold2fmap["BOLD-fieldmap
                 transform"]:::opt
      boldref_hmc["Initial BOLD
                   Reference"]
      fmap'["Preprocessed
             Fieldmap"]:::opt

      T1w ----> coreg
      bold --> boldref_hmc ---> hmc
      bold --> hmc
      boldref_hmc --> boldref_coreg --> coreg
      fmap -.-> fmap' -.-> boldref_coreg
      boldref_hmc & fmap' -..-> bold2fmap
      sbref -.-> boldref_coreg
    boldref_coreg ~~~ bold2fmap -.-> boldref_coreg
    end